Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 29
Found at i:739840 original size:10 final size:11
Alignment explanation
Indices: 739825--739869 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
739815 TTTCAATTCC
739825 TTTATCTT-TT
1 TTTATCTTGTT
739835 TTTATCTTGTT
1 TTTATCTTGTT
*
739846 TTAATCTTGTT
1 TTTATCTTGTT
*
739857 TCTTACCTTGTT
1 T-TTATCTTGTT
739869 T
1 T
739870 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.11, C:0.13, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:739867 original size:23 final size:21
Alignment explanation
Indices: 739828--739869 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
739818 CAATTCCTTT
*
739828 ATCTTTTTTTATCTTGTTTTA
1 ATCTTTTTTTACCTTGTTTTA
739849 ATCTTGTTTCTTACCTTGTTT
1 ATCTT-TTT-TTACCTTGTTT
739870 CCAGCACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (21 bp):
ATCTTTTTTTACCTTGTTTTA
Found at i:741490 original size:19 final size:20
Alignment explanation
Indices: 741469--741512 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
741459 TAACTATTTA
*
741469 TTTTATCTTTCATTATTAAT
1 TTTTATCTTTCATTATTAAC
*
741489 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAC
741508 TTTTA
1 TTTTA
741513 ATTTTTCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAC
Found at i:744826 original size:24 final size:24
Alignment explanation
Indices: 744797--744846 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
744787 TGGTGGTTGA
*
744797 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
744821 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
744845 TT
1 TT
744847 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:750288 original size:8 final size:8
Alignment explanation
Indices: 750277--750307 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
750267 ATAAATCCTA
750277 AAAAAGTG
1 AAAAAGTG
750285 AAAAAGTG
1 AAAAAGTG
*
750293 AAAGAGTG
1 AAAAAGTG
750301 AAAAAGT
1 AAAAAGT
750308 TTTCCCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (8 bp):
AAAAAGTG
Found at i:757839 original size:15 final size:15
Alignment explanation
Indices: 757819--757875 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
757809 TGGTCGGGTC
*
757819 ATTTTTTATTTTATTT
1 ATTTTATATTTTA-TT
757835 ATTTTATATTTTATT
1 ATTTTATATTTTATT
757850 A-TTTACTA-TTTATT
1 ATTTTA-TATTTTATT
757864 ATTATTA-ATTTT
1 ATT-TTATATTTT
757876 GTTTACACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 12 0.33
15 9 0.25
16 15 0.42
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTATATTTTATT
Found at i:757844 original size:7 final size:8
Alignment explanation
Indices: 757819--757866 Score: 50
Period size: 7 Copynumber: 6.4 Consensus size: 8
757809 TGGTCGGGTC
757819 ATTTT-TT
1 ATTTTATT
757826 ATTTTATTT
1 ATTTTA-TT
757835 ATTTTA-T
1 ATTTTATT
757842 ATTTTATT
1 ATTTTATT
*
757850 A-TTTACT
1 ATTTTATT
757857 A-TTTATT
1 ATTTTATT
757864 ATT
1 ATT
757867 ATTAATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
7 24 0.69
8 3 0.09
9 8 0.23
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTTTATT
Found at i:759189 original size:28 final size:29
Alignment explanation
Indices: 759146--759234 Score: 117
Period size: 28 Copynumber: 3.1 Consensus size: 29
759136 TTATTTGTAA
*
759146 TTATTATTTTAGTCCTTTAAGTTTCTATT
1 TTATTGTTTTAGTCCTTTAAGTTTCTATT
* *
759175 TTATTG-TTTAGTCCTTTAAGTGTCTATAA
1 TTATTGTTTTAGTCCTTTAAGTTTCTAT-T
* *
759204 TTATTGTTTTAGGCCTTTAAGTTTCTGTT
1 TTATTGTTTTAGTCCTTTAAGTTTCTATT
759233 TT
1 TT
759235 TGATATTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
28 20 0.39
29 13 0.25
30 18 0.35
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.58
Consensus pattern (29 bp):
TTATTGTTTTAGTCCTTTAAGTTTCTATT
Found at i:759244 original size:30 final size:30
Alignment explanation
Indices: 759150--759318 Score: 116
Period size: 30 Copynumber: 5.7 Consensus size: 30
759140 TTGTAATTAT
*
759150 TATTTTAGTCCTTTAAGTTTC--TATTTTA
1 TATTTTAGTCCTTTAAGTTTCTGTATTTGA
* * *
759178 T-TGTTTAGTCCTTTAAGTGTCTATAATT-A
1 TAT-TTTAGTCCTTTAAGTTTCTGTATTTGA
* * *
759207 TTGTTTTAGGCCTTTAAGTTTCTGTTTTTGA
1 -TATTTTAGTCCTTTAAGTTTCTGTATTTGA
* * * *
759238 TATTTTAGCCCCTTCAA-TTTTTGTATTTGC
1 TATTTTAG-TCCTTTAAGTTTCTGTATTTGA
* * *
759268 TA-TTTAGTCCCTTAAGTTCCTGTATTTGC
1 TATTTTAGTCCTTTAAGTTTCTGTATTTGA
* * *
759297 TATTTCAGTGCATTAAGTTTCT
1 TATTTTAGTCCTTTAAGTTTCT
759319 ATTTTTCTCC
Statistics
Matches: 110, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 23 0.21
29 19 0.17
30 59 0.54
31 8 0.07
ACGTcount: A:0.19, C:0.14, G:0.13, T:0.54
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGTTTCTGTATTTGA
Found at i:759291 original size:29 final size:30
Alignment explanation
Indices: 759259--759315 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
759249 CTTCAATTTT
*
759259 TGTATTTGCTATTT-AGTCCCTTAAGTTCC
1 TGTATTTGCTATTTCAGTCCATTAAGTTCC
*
759288 TGTATTTGCTATTTCAGTGCATTAAGTT
1 TGTATTTGCTATTTCAGTCCATTAAGTT
759316 TCTATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (30 bp):
TGTATTTGCTATTTCAGTCCATTAAGTTCC
Found at i:763790 original size:20 final size:20
Alignment explanation
Indices: 763761--763803 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
763751 TTTCCAGCAC
* *
763761 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATACTAA
*
763781 ATGCATCTATATGATACTAA
1 ATGCAACTATATGATACTAA
763801 ATG
1 ATG
763804 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATACTAA
Found at i:766064 original size:22 final size:23
Alignment explanation
Indices: 766021--766064 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
766011 GACCCGACCC
*
766021 GTTGACTGTTGATCGGTTTGACA
1 GTTGACTGTTGATCGGTATGACA
766044 GTTGACT-TTGA-CTGGTATGAC
1 GTTGACTGTTGATC-GGTATGAC
766065 CTTTGATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.58
23 7 0.37
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.39
Consensus pattern (23 bp):
GTTGACTGTTGATCGGTATGACA
Found at i:766070 original size:16 final size:14
Alignment explanation
Indices: 766044--766086 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
766034 CGGTTTGACA
766044 GTTGACTTTGACTG
1 GTTGACTTTGACTG
*
766058 GTATGACCTTTGA-TT
1 GT-TGA-CTTTGACTG
766073 GTTGACTTTGACTG
1 GTTGACTTTGACTG
766087 AAAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (14 bp):
GTTGACTTTGACTG
Found at i:768948 original size:43 final size:43
Alignment explanation
Indices: 768900--768986 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
768890 TTCCCCACGG
768900 CGTAAAGATGGTGAGCCAGGAGCCCAATGCCCAAACCCAACAC
1 CGTAAAGATGGTGAGCCAGGAGCCCAATGCCCAAACCCAACAC
768943 CGTAAAGATGGTGAGCCAGGAGCCCAATGCCCAAACCCAACAC
1 CGTAAAGATGGTGAGCCAGGAGCCCAATGCCCAAACCCAACAC
768986 C
1 C
768987 CAAATCTCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.33, G:0.23, T:0.09
Consensus pattern (43 bp):
CGTAAAGATGGTGAGCCAGGAGCCCAATGCCCAAACCCAACAC
Found at i:775478 original size:19 final size:19
Alignment explanation
Indices: 775429--775479 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
775419 GTGAGCGGTG
775429 ATTTACT-AAAAATGAGAA
1 ATTTACTAAAAAATGAGAA
* * *
775447 AATTAATATAAAAATGGGAA
1 ATTTACTA-AAAAATGAGAA
775467 ATTTACTAAAAAA
1 ATTTACTAAAAAA
775480 ACAACATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 16 0.62
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (19 bp):
ATTTACTAAAAAATGAGAA
Found at i:777506 original size:36 final size:36
Alignment explanation
Indices: 777450--777554 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
777440 TGGGCTCTCT
*
777450 ATCCTTGGCGAGGAGATGAAGGGTGAAGAATTGGTA
1 ATCCATGGCGAGGAGATGAAGGGTGAAGAATTGGTA
*
777486 ATCCATGGTGAGGAGATGAAGGGTGAAGAATTGGTA
1 ATCCATGGCGAGGAGATGAAGGGTGAAGAATTGGTA
777522 A-CACATGGCGAGGAGATGAAGGGTGAAGAATTG
1 ATC-CATGGCGAGGAGATGAAGGGTGAAGAATTG
777555 CTAAACAGGA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 1 0.02
36 64 0.98
ACGTcount: A:0.33, C:0.08, G:0.39, T:0.20
Consensus pattern (36 bp):
ATCCATGGCGAGGAGATGAAGGGTGAAGAATTGGTA
Found at i:780451 original size:104 final size:104
Alignment explanation
Indices: 780324--780529 Score: 385
Period size: 104 Copynumber: 2.0 Consensus size: 104
780314 GGGGGCAAGA
780324 AAGGTTGGTTTTACTCCTTTGGTTTGTGGTTGATGGTTTTCATATAATTGAATTGCATGATTTTC
1 AAGGTTGGTTTTACTCCTTTGGTTTGTGGTTGATGGTTTTCATATAATTGAATTGCATGATTTTC
* **
780389 AAAGAGGGTTATAAATGGTTGACTTTACTATTTCTTACG
66 AAAGAGGATTATAAACAGTTGACTTTACTATTTCTTACG
780428 AAGGTTGGTTTTACTCCTTTGGTTTGTGGTTGATGGTTTTCATATAATTGAATTGCATGATTTTC
1 AAGGTTGGTTTTACTCCTTTGGTTTGTGGTTGATGGTTTTCATATAATTGAATTGCATGATTTTC
780493 AAAGAGGATTATAAACAGTTGACTTTACTATTTCTTA
66 AAAGAGGATTATAAACAGTTGACTTTACTATTTCTTA
780530 TGTGGTGACT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (104 bp):
AAGGTTGGTTTTACTCCTTTGGTTTGTGGTTGATGGTTTTCATATAATTGAATTGCATGATTTTC
AAAGAGGATTATAAACAGTTGACTTTACTATTTCTTACG
Found at i:781151 original size:19 final size:20
Alignment explanation
Indices: 781127--781164 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
781117 ATTTGAATCC
781127 TTTGTTAATTATGC-TTTGG
1 TTTGTTAATTATGCGTTTGG
781146 TTTGTTAATTATGCGTTTG
1 TTTGTTAATTATGCGTTTG
781165 AAGTTGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (20 bp):
TTTGTTAATTATGCGTTTGG
Found at i:787586 original size:17 final size:16
Alignment explanation
Indices: 787564--787632 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
787554 CCGTGTCCCG
*
787564 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
787581 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
787596 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
787613 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
787628 ACCCG
1 ACCCG
787633 ATACCCGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:787596 original size:15 final size:15
Alignment explanation
Indices: 787576--787632 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
787566 CCGGATGTTA
787576 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
787591 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
787607 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
787623 CGGGTACCCG
1 CGGGTACCCG
787633 ATACCCGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:787600 original size:32 final size:32
Alignment explanation
Indices: 787564--787632 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
787554 CCGTGTCCCG
787564 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
787596 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
787628 ACCCG
1 ACCCG
787633 ATACCCGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:789205 original size:3 final size:3
Alignment explanation
Indices: 789197--789238 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
789187 TTGTTTTGTA
* * *
789197 AAT AAT AAT AAT AAT TAT AAT -AT AAT AAT ATT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
789239 TATAGGTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:789223 original size:17 final size:17
Alignment explanation
Indices: 789201--789235 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
789191 TTTGTAAATA
789201 ATAATAATAATTA-TAAT
1 ATAATAAT-ATTATTAAT
789218 ATAATAATATTATTAAT
1 ATAATAATATTATTAAT
789235 A
1 A
789236 ATATATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATATTATTAAT
Found at i:789223 original size:20 final size:20
Alignment explanation
Indices: 789198--789240 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
789188 TGTTTTGTAA
789198 ATAATAATAATAATT-ATAAT
1 ATAATAAT-ATAATTAATAAT
*
789218 ATAATAATATTATTAATAAT
1 ATAATAATATAATTAATAAT
789238 ATA
1 ATA
789241 TAGGTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAATATAATTAATAAT
Found at i:789698 original size:140 final size:140
Alignment explanation
Indices: 789360--789812 Score: 547
Period size: 140 Copynumber: 3.2 Consensus size: 140
789350 TTCAAGCTGC
* * * * * * *
789360 GAGTTCTTTTCATTACAAATTATCTACTAGAAATGTTGATCCCTCGAGTGAGGCATCGCTGATTC
1 GAGTTCTTCTCATTATAAACTCTCTACTAGAAATATTAATCCATCGAGTGAGGCATCGCTGATTC
* ** *
789425 AACTCCAAAATTTGATGAATCGAGCT-AAGGTTGAACAAGTTTTTCTCATTATGAACTT-TTCTC
66 AACT-CAATATACGATGAATCGAG-TAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
789488 CCTC-ATCGGAT
129 CCTCTATCGGAT
* * * * *
789499 GAGTTCTTCTCATTATGAAC-C-CTACATTGGAAATATTAATACATCGAGTAAGGCGTCGCTGAT
1 GAGTTCTTCTCATTATAAACTCTCTAC--TAGAAATATTAATCCATCGAGTGAGGCATCGCTGAT
* * * * *
789562 TCAACTCTATATACGATGAATCAAGTAAATGTTGAATAAGTTCTTCTCATTATGAACTTCTTTTC
64 TCAACTCAATATACGATGAATCGAGTAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
789627 CCTCTATCGGAT
129 CCTCTATCGGAT
* * **
789639 GAGTTCTTCTCATTATAAACTCTCTACTAGAAATTTTAATCCTTTAAGTGAGGCATCGCTGATTC
1 GAGTTCTTCTCATTATAAACTCTCTACTAGAAATATTAATCCATCGAGTGAGGCATCGCTGATTC
* * *
789704 AACTCCATATGCGATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
66 AACTCAATATACGATGAATCGAGTAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
789769 TCTATCGGAT
131 TCTATCGGAT
* * * *
789779 GAGTTATTCTCATTATGAACTCTCCACTGGAAAT
1 GAGTTCTTCTCATTATAAACTCTCTACTAGAAAT
789813 GTTGATTGGT
Statistics
Matches: 266, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
137 5 0.02
138 43 0.16
139 59 0.22
140 154 0.58
141 1 0.00
142 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (140 bp):
GAGTTCTTCTCATTATAAACTCTCTACTAGAAATATTAATCCATCGAGTGAGGCATCGCTGATTC
AACTCAATATACGATGAATCGAGTAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
TCTATCGGAT
Found at i:791800 original size:40 final size:40
Alignment explanation
Indices: 791756--791865 Score: 177
Period size: 40 Copynumber: 2.8 Consensus size: 40
791746 AGGACACTAA
*
791756 GTGTATATGATGGGCACGACCTTTTGTGTAATACACTTCG
1 GTGTATATGATGGGCACGACCTTATGTGTAATACACTTCG
* *
791796 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTTG
1 GTGTATATGATGGGCACGACCTTATGTGTAATACACTTCG
791836 GTGTATAT-AGTGGGCACGACCTTATGTGTA
1 GTGTATATGA-TGGGCACGACCTTATGTGTA
791866 GCACTACGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (40 bp):
GTGTATATGATGGGCACGACCTTATGTGTAATACACTTCG
Found at i:792619 original size:54 final size:54
Alignment explanation
Indices: 792475--792602 Score: 247
Period size: 54 Copynumber: 2.4 Consensus size: 54
792465 TACAGACTGG
*
792475 TAAGGCGTGCCCACGCCTTAACTTAAAACCTTTTCTGCAGTATCTCAGAATGAA
1 TAAGCCGTGCCCACGCCTTAACTTAAAACCTTTTCTGCAGTATCTCAGAATGAA
792529 TAAGCCGTGCCCACGCCTTAACTTAAAACCTTTTCTGCAGTATCTCAGAATGAA
1 TAAGCCGTGCCCACGCCTTAACTTAAAACCTTTTCTGCAGTATCTCAGAATGAA
792583 TAAGCCGTGCCCACGCCTTA
1 TAAGCCGTGCCCACGCCTTA
792603 TTCAAAAACC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (54 bp):
TAAGCCGTGCCCACGCCTTAACTTAAAACCTTTTCTGCAGTATCTCAGAATGAA
Found at i:796198 original size:30 final size:32
Alignment explanation
Indices: 796134--796208 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
796124 AATGGATTTA
* * * *
796134 TTTAGTGATCAAATTATATACATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAACATTTGGAAAAG
796166 TTTAGTGACCAAAGTATAAAC-TTT-GAAAAG
1 TTTAGTGACCAAAGTATAAACATTTGGAAAAG
*
796196 TTTAGGGACCAAA
1 TTTAGTGACCAAA
796209 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 17 0.45
31 3 0.08
32 18 0.47
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (32 bp):
TTTAGTGACCAAAGTATAAACATTTGGAAAAG
Found at i:796224 original size:30 final size:31
Alignment explanation
Indices: 796156--796224 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
796146 ATTATATACA
* * *
796156 TTTGGTAAAGTTTAGTGACCAAAGTATAAAC
1 TTTGGAAAAGTTTAGGGACCAAAATATAAAC
* *
796187 TTT-GAAAAGTTTAGGGACCAAAATGT-AAT
1 TTTGGAAAAGTTTAGGGACCAAAATATAAAC
796216 TTTGGAAAA
1 TTTGGAAAA
796225 ATTACAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.16
30 24 0.75
31 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (31 bp):
TTTGGAAAAGTTTAGGGACCAAAATATAAAC
Found at i:797709 original size:40 final size:40
Alignment explanation
Indices: 797665--797774 Score: 202
Period size: 40 Copynumber: 2.8 Consensus size: 40
797655 AGGACACTAA
797665 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
* *
797705 GTGTATATGGTGGGCATGACCTTATGTGTAATACACTTTG
1 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
797745 GTGTATATGGTGGGCACGACCTTATGTGTA
1 GTGTATATGGTGGGCACGACCTTATGTGTA
797775 GCTCTACGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.35
Consensus pattern (40 bp):
GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
Found at i:799435 original size:18 final size:18
Alignment explanation
Indices: 799414--799448 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
799404 TCGAACCATT
799414 TTTTCCTTT-TCTTTTTTC
1 TTTT-CTTTCTCTTTTTTC
799432 TTTTCTTTCTCTTTTTT
1 TTTTCTTTCTCTTTTTT
799449 TAGGTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTCTTTTTTC
Found at i:802466 original size:7 final size:7
Alignment explanation
Indices: 802454--802497 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
802444 TTTTGGAATG
802454 TAAAGAA
1 TAAAGAA
802461 TAAAGAA
1 TAAAGAA
802468 TAAAGAA
1 TAAAGAA
802475 TAAAGAA
1 TAAAGAA
802482 TAAAGAA
1 TAAAGAA
802489 TAAAGAA
1 TAAAGAA
802496 TA
1 TA
802498 TGATGCAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
TAAAGAA
Found at i:802777 original size:12 final size:12
Alignment explanation
Indices: 802760--802784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
802750 TAACTTTCCA
802760 ACTCCTCAATCC
1 ACTCCTCAATCC
802772 ACTCCTCAATCC
1 ACTCCTCAATCC
802784 A
1 A
802785 TTCAAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.48, G:0.00, T:0.24
Consensus pattern (12 bp):
ACTCCTCAATCC
Found at i:811048 original size:31 final size:31
Alignment explanation
Indices: 811013--811088 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
811003 TAAGGAGACC
811013 CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
811044 CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
*
811075 CTTGAGTAGGCTCT
1 CTTGGGTAGGCTCT
811089 CAGTCCCCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.28
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGAACTTT
Found at i:813565 original size:11 final size:11
Alignment explanation
Indices: 813549--813573 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
813539 AACATCAAAG
813549 AAAATAAAAAT
1 AAAATAAAAAT
813560 AAAATAAAAAT
1 AAAATAAAAAT
813571 AAA
1 AAA
813574 TACAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:814978 original size:22 final size:23
Alignment explanation
Indices: 814953--815002 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
814943 GTTAGGTTTA
*
814953 GGTTAGGGTAGG-CTTCGGGTCG
1 GGTTAGGGTAGGACTCCGGGTCG
* * *
814975 GGTTTGGTTTGGACTCCGGGTCG
1 GGTTAGGGTAGGACTCCGGGTCG
814998 GGTTA
1 GGTTA
815003 TTTTTTGGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.08, C:0.14, G:0.46, T:0.32
Consensus pattern (23 bp):
GGTTAGGGTAGGACTCCGGGTCG
Found at i:821393 original size:15 final size:15
Alignment explanation
Indices: 821373--821414 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
821363 CTTCATGGGG
*
821373 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
821388 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
821403 AAAGAAGGAAAA
1 TAAGAA-GAAAA
821415 AGAAAGCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.57, C:0.12, G:0.21, T:0.10
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Found at i:825279 original size:25 final size:26
Alignment explanation
Indices: 825252--825320 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
825242 AGAAGTAAAG
825252 AAAGGAGAAGGGACACCGAAGACGGA
1 AAAGGAGAAGGGACACCGAAGACGGA
* * * ** * *
825278 AAAAGAGAA-AGAAAAGGAAGAGGGT
1 AAAGGAGAAGGGACACCGAAGACGGA
825303 AAAGGAGAAGGGACACCG
1 AAAGGAGAAGGGACACCG
825321 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.51, C:0.10, G:0.38, T:0.01
Consensus pattern (26 bp):
AAAGGAGAAGGGACACCGAAGACGGA
Found at i:825351 original size:39 final size:39
Alignment explanation
Indices: 825289--825405 Score: 127
Period size: 39 Copynumber: 3.0 Consensus size: 39
825279 AAAGAGAAAG
825289 AAAAGGAAGAGG-GTAAAGGAGAAGGGACACCGCAAAGGA
1 AAAAGGAAGAGGAG-AAAGGAGAAGGGACACCGCAAAGGA
*
825328 AAAAGGAAGAGGAGAAAGAAGAAGGGACACCG-AAGAGGGA
1 AAAAGGAAGAGGAGAAAGGAGAAGGGACACCGCAA-A-GGA
* *
825368 AAGAAAGAA-A-GA-AAAGGAGGAGGGAACACCGCAAAGGA
1 AA-AAGGAAGAGGAGAAAGGAGAAGGG-ACACCGCAAAGGA
825406 GGAGGACGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
38 15 0.22
39 39 0.57
40 9 0.13
41 5 0.07
ACGTcount: A:0.52, C:0.09, G:0.38, T:0.01
Consensus pattern (39 bp):
AAAAGGAAGAGGAGAAAGGAGAAGGGACACCGCAAAGGA
Found at i:825918 original size:12 final size:12
Alignment explanation
Indices: 825898--825928 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
825888 TAATCCCGAG
*
825898 TTTGTTTTTTCA
1 TTTGATTTTTCA
825910 TTTGATTTTTCA
1 TTTGATTTTTCA
825922 TTTGATT
1 TTTGATT
825929 ATCAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.10, T:0.71
Consensus pattern (12 bp):
TTTGATTTTTCA
Found at i:827416 original size:2 final size:2
Alignment explanation
Indices: 827409--827478 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
827399 GTCAATCTGC
827409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
827451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
827479 ATTTCCGAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:827624 original size:85 final size:84
Alignment explanation
Indices: 827526--827833 Score: 413
Period size: 85 Copynumber: 3.6 Consensus size: 84
827516 GTCTTTTTAA
* * ** * * *
827526 ATGACGTGTGCTTCAATGACATGCAATGTAAGTCATATATGCGTGTCATATATTTATGACACACA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACAAA
* *
827591 AATGTATGTCAAGC-AGATTT
66 AATGTGTGTC-ATCTA-ATTT
* * *
827611 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATACGTGTAATAAATTTATGA-AGCAT
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACA-CAA
827675 AAATGTGTGTCATCTTAATTT
65 AAATGTGTGTCATC-TAATTT
* * *
827696 ATGACGAGGGCTTTAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCAAA
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACAAA
827761 AATGTGTGTCATCTTAATTT
66 AATGTGTGTCATC-TAATTT
*
827781 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAAT
1 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAAT
827834 GTGCGTCATA
Statistics
Matches: 199, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
84 3 0.02
85 195 0.98
86 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (84 bp):
ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACAAA
AATGTGTGTCATCTAATTT
Found at i:827830 original size:13 final size:13
Alignment explanation
Indices: 827812--827869 Score: 89
Period size: 13 Copynumber: 4.5 Consensus size: 13
827802 CGCAATGTAA
*
827812 GTCATACATGCGC
1 GTCATAAATGCGC
*
827825 GTCATAAATGTGC
1 GTCATAAATGCGC
827838 GTCATAAATGCGC
1 GTCATAAATGCGC
*
827851 ATCATAAATGCGC
1 GTCATAAATGCGC
827864 GTCATA
1 GTCATA
827870 GATTTATTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:828233 original size:14 final size:14
Alignment explanation
Indices: 828180--828229 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
828170 AACTTGGTTC
828180 GAGTCAACCCGTCT
1 GAGTCAACCCGTCT
* *
828194 GAGTTAACCCGTAT
1 GAGTCAACCCGTCT
* *
828208 GATTCAACTCGTCT
1 GAGTCAACCCGTCT
828222 GAGTCAAC
1 GAGTCAAC
828230 TCGTTGACTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (14 bp):
GAGTCAACCCGTCT
Found at i:833348 original size:17 final size:16
Alignment explanation
Indices: 833324--833357 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
833314 GCAAAACATC
833324 AAATAAAATAAAAACA
1 AAATAAAATAAAAACA
*
833340 AAATAAAAATAAATACA
1 AAAT-AAAATAAAAACA
833357 A
1 A
833358 TTGTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAAAATAAAAACA
Found at i:834847 original size:24 final size:24
Alignment explanation
Indices: 834819--834869 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
834809 GCAGTTTTCC
*
834819 TTTTTTTGCACTTGTAATATATGTA
1 TTTTTTTG-AATTGTAATATATGTA
*
834844 TTTTTTTGAATTGTAATATTTGTA
1 TTTTTTTGAATTGTAATATATGTA
834868 TT
1 TT
834870 GGGTTATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTTTTTGAATTGTAATATATGTA
Found at i:841915 original size:20 final size:20
Alignment explanation
Indices: 841886--841933 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
841876 GAGTTAATTA
*
841886 AAAATATGTTTGAAGT-CTTT
1 AAAATATGTTT-AAATCCTTT
*
841906 AAAATGTGTTTAAATCCTTT
1 AAAATATGTTTAAATCCTTT
841926 AAAATATG
1 AAAATATG
841934 AAAAACACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (20 bp):
AAAATATGTTTAAATCCTTT
Found at i:843436 original size:20 final size:19
Alignment explanation
Indices: 843395--843437 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
843385 AATGATTTTC
* * *
843395 TTTTGAAAACTAAATTAGA
1 TTTTGAAAACAAAATGAAA
843414 TTTTGAAAAACAAAATGAAA
1 TTTTG-AAAACAAAATGAAA
843434 TTTT
1 TTTT
843438 AAATAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:845809 original size:20 final size:20
Alignment explanation
Indices: 845786--845823 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
845776 TATGAAAATT
845786 AAATTAAATTTTGAAAAACA
1 AAATTAAATTTTGAAAAACA
845806 AAATTAAATTTTGAAAAA
1 AAATTAAATTTTGAAAAA
845824 TTATTTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATTAAATTTTGAAAAACA
Found at i:847403 original size:20 final size:20
Alignment explanation
Indices: 847380--847424 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
847370 ATTAGTTTTG
847380 AAACTTTCGT-AAAAGTTTCA
1 AAACTTTC-TCAAAAGTTTCA
*
847400 AAACTTTCTCCAAAGTTTCA
1 AAACTTTCTCAAAAGTTTCA
847420 AAACT
1 AAACT
847425 ACATGTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (20 bp):
AAACTTTCTCAAAAGTTTCA
Found at i:849620 original size:27 final size:27
Alignment explanation
Indices: 849586--849775 Score: 137
Period size: 27 Copynumber: 6.7 Consensus size: 27
849576 AATATGATGG
849586 ATAATATCAATAGTTGAATGAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* *
849613 ATAATATCAATAATTGAATTAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* * * *
849640 TTAATATCAATATTTCAATTAATATGATGGA
1 ATAATATCAATAGTTGAA-TGA-ATG-T-GA
** * * * * *
849671 TATTTGTTGGTGCTATATTTTAATGAATATGA
1 -A--TAAT-AT-CAATAGTTGAATGAATGTGA
*
849703 TTAATATCAATAGTTGAATGAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* *
849730 ATAATATCAATAGTTTAATTAATGTGA
1 ATAATATCAATAGTTGAATGAATGTGA
* *
849757 TTAATATCAATATTTGAAT
1 ATAATATCAATAGTTGAAT
849776 TAATATGATG
Statistics
Matches: 126, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
27 96 0.76
28 3 0.02
29 5 0.04
30 1 0.01
31 2 0.02
32 2 0.02
33 1 0.01
34 4 0.03
35 3 0.02
36 9 0.07
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (27 bp):
ATAATATCAATAGTTGAATGAATGTGA
Found at i:849645 original size:54 final size:54
Alignment explanation
Indices: 849587--849813 Score: 174
Period size: 54 Copynumber: 4.1 Consensus size: 54
849577 ATATGATGGA
849587 TAATATCAATAGTTGAATGAATGTGAATAATATCAATAATTGAATTAATGTGAT
1 TAATATCAATAGTTGAATGAATGTGAATAATATCAATAATTGAATTAATGTGAT
* * * ** * * * * * *
849641 TAATATCAATATTTCAATTAATATGATGGATATTTGTTGGTGCTATATTTTAATGAATATGAT
1 TAATATCAATAGTTGAA-TGA-ATG-T-GA-A--TAAT-AT-CAATAATTGAATTAATGTGAT
* *
849704 TAATATCAATAGTTGAATGAATGTGAATAATATCAATAGTTTAATTAATGTGAT
1 TAATATCAATAGTTGAATGAATGTGAATAATATCAATAATTGAATTAATGTGAT
* * * * *
849758 TAATATCAATATTTGAATTAATATG-ATGGATATTAATAATTGAA-TAATG-GA-
1 TAATATCAATAGTTGAATGAATGTGAAT-AATATCAATAATTGAATTAATGTGAT
849809 TAATA
1 TAATA
849814 ATTCAACTTA
Statistics
Matches: 135, Mismatches: 28, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
51 5 0.04
52 2 0.01
53 7 0.05
54 66 0.49
55 3 0.02
56 5 0.04
57 1 0.01
58 3 0.02
59 3 0.02
60 1 0.01
61 5 0.04
62 3 0.02
63 31 0.23
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.41
Consensus pattern (54 bp):
TAATATCAATAGTTGAATGAATGTGAATAATATCAATAATTGAATTAATGTGAT
Found at i:849776 original size:27 final size:27
Alignment explanation
Indices: 849685--849813 Score: 122
Period size: 27 Copynumber: 4.9 Consensus size: 27
849675 TGTTGGTGCT
* * *
849685 ATATTTTAATGAATATGATTAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
* * *
849712 ATAGTTGAATGAATGTGAATAATATCA
1 ATATTTGAATTAATGTGATTAATATCA
849739 ATAGTTT-AATTAATGTGATTAATATCA
1 ATA-TTTGAATTAATGTGATTAATATCA
* ** *
849766 ATATTTGAATTAATATGATGGATATTA
1 ATATTTGAATTAATGTGATTAATATCA
*
849793 ATAATTGAA-TAATG-GA-TAATA
1 ATATTTGAATTAATGTGATTAATA
849814 ATTCAACTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
24 3 0.04
25 2 0.02
26 7 0.08
27 71 0.84
28 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (27 bp):
ATATTTGAATTAATGTGATTAATATCA
Found at i:857975 original size:14 final size:15
Alignment explanation
Indices: 857957--857996 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
857947 TGAATCGAAC
857957 AAGTTGACTCAG-AT
1 AAGTTGACTCAGAAT
*
857971 GAGTTGACTC-GAAT
1 AAGTTGACTCAGAAT
857985 AAGTTGACTCAG
1 AAGTTGACTCAG
857997 TCCCGATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (15 bp):
AAGTTGACTCAGAAT
Found at i:866479 original size:21 final size:21
Alignment explanation
Indices: 866453--866499 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
866443 TGCTTTTGCT
866453 AGTTGGTTCCCACTTCTTAAA
1 AGTTGGTTCCCACTTCTTAAA
866474 AGTTGGTTCCCACTTCTTAAA
1 AGTTGGTTCCCACTTCTTAAA
866495 AGTTG
1 AGTTG
866500 CTTCAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
AGTTGGTTCCCACTTCTTAAA
Found at i:868163 original size:38 final size:40
Alignment explanation
Indices: 868103--868192 Score: 136
Period size: 38 Copynumber: 2.4 Consensus size: 40
868093 AATGTATTCG
868103 GTTTTGAAAAC--A-TTTTTGAAAACATATATAATATATA
1 GTTTTGAAAACATATTTTTTGAAAACATATATAATATATA
*
868140 GTTTT-AAAA-ATATTTTTTGAAAACTTATATAATATATA
1 GTTTTGAAAACATATTTTTTGAAAACATATATAATATATA
868178 GTTTTGAAAACATAT
1 GTTTTGAAAACATAT
868193 ATAATATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
36 4 0.09
37 6 0.13
38 29 0.62
39 4 0.09
40 4 0.09
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (40 bp):
GTTTTGAAAACATATTTTTTGAAAACATATATAATATATA
Found at i:868199 original size:23 final size:25
Alignment explanation
Indices: 868154--868215 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
868144 TAAAAATATT
*
868154 TTTTGAAAACTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
868179 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAG
*
868204 TTTTAAAAACAT
1 TTTTGAAAACAT
868216 TTTTTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (25 bp):
TTTTGAAAACATATATAATATATAG
Found at i:868218 original size:63 final size:63
Alignment explanation
Indices: 868116--868253 Score: 249
Period size: 63 Copynumber: 2.2 Consensus size: 63
868106 TTGAAAACAT
* * *
868116 TTTTGAAAACATATATAATATATAGTTTTAAAAATATTTTTTGAAAACTTATATAATATATAG
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTTCAAAACATATATAATATATAG
868179 TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTTCAAAACATATATAATATATAG
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTTCAAAACATATATAATATATAG
868242 TTTTGAAAACAT
1 TTTTGAAAACAT
868254 TTTTTAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (63 bp):
TTTTGAAAACATATATAATATATAGTTTTAAAAACATTTTTTCAAAACATATATAATATATAG
Found at i:868238 original size:36 final size:38
Alignment explanation
Indices: 868179--868317 Score: 203
Period size: 38 Copynumber: 3.7 Consensus size: 38
868169 TAATATATAG
868179 TTTTGAAAACATATATAATATATAGTTTTAAAAACATT
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATT
* *
868217 TTTTCAAAACATATATAATATATAGTTTTGAAAACATT
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATT
* *
868255 TTTT-AAAA-ATATATAATATATAGTTTAAAAAATATT
1 TTTTGAAAACATATATAATATATAGTTTTAAAAACATT
* *
868291 TTTTG-AAATATATATATTATATAGTTT
1 TTTTGAAAACATATATAATATATAGTTT
868318 ATATTATTAT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
36 32 0.34
37 21 0.23
38 40 0.43
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTGAAAACATATATAATATATAGTTTTAAAAACATT
Found at i:868327 original size:3 final size:3
Alignment explanation
Indices: 868319--868343 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
868309 ATATAGTTTA
868319 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
868344 TATGATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:869788 original size:21 final size:22
Alignment explanation
Indices: 869747--869788 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
869737 TTATTTTCCC
*
869747 TTTTTTATATTTAGTTTATTTA
1 TTTTTTATACTTAGTTTATTTA
869769 TTTTTTAT-CTTA-TTTCATTT
1 TTTTTTATACTTAGTTT-ATTT
869789 TCCCTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTATACTTAGTTTATTTA
Found at i:869850 original size:39 final size:38
Alignment explanation
Indices: 869807--869942 Score: 102
Period size: 41 Copynumber: 3.4 Consensus size: 38
869797 ATTTTTTTTA
869807 TTTTTTTGTTTTTTTTCCTTTGATTTATTTA--ATTAT
1 TTTTTTTGTTTTTTTTCCTTTGATTTATTTATTATTAT
*
869843 TATTTTTT-ATTTTTTTCCTTTGATTTGTATTTGTATT-TATAT
1 T-TTTTTTGTTTTTTTTCCTTTGA-TT-TA-TT-TATTAT-TAT
* * *
869885 TTTTTATTTTATTTTTTTCATTTGATTTATCATT-TTAGTAT
1 TTTTT-TTGT-TTTTTTTCCTTTGATTTAT--TTATTATTAT
869926 TTTTTTATGTTTTTTTT
1 TTTTTT-TGTTTTTTTT
869943 ATTTAATATT
Statistics
Matches: 80, Mismatches: 5, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
36 15 0.19
37 8 0.10
38 2 0.03
39 2 0.03
40 10 0.12
41 18 0.22
42 9 0.11
43 3 0.04
44 13 0.16
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (38 bp):
TTTTTTTGTTTTTTTTCCTTTGATTTATTTATTATTAT
Found at i:869856 original size:36 final size:35
Alignment explanation
Indices: 869786--869894 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
869776 TCTTATTTCA
*
869786 TTTTCCCTTTGATTT-TTT-TTATT-TTTTTGT-TT
1 TTTTTCCTTTGATTTATTTATTATTATTTTT-TATT
869818 TTTTTCCTTTGATTTATTTAATTATTATTTTTTATT
1 TTTTTCCTTTGATTTATTT-ATTATTATTTTTTATT
869854 TTTTTCCTTTGATTTGTATTTGTATT-TATATTTTTTATT
1 TTTTTCCTTTGA-TT-TA-TT-TATTAT-TATTTTTTATT
869893 TT
1 TT
869895 ATTTTTTTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
32 14 0.21
33 3 0.05
35 6 0.09
36 19 0.29
37 2 0.03
38 3 0.05
39 18 0.27
40 1 0.02
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (35 bp):
TTTTTCCTTTGATTTATTTATTATTATTTTTTATT
Found at i:870808 original size:24 final size:24
Alignment explanation
Indices: 870787--870850 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
870777 TTTATTTATG
*
870787 TTCGTTCCTATATGTTTGTTTACT
1 TTCGTTCGTATATGTTTGTTTACT
870811 TTCGTTCGTATATGTTTGTTTACT
1 TTCGTTCGTATATGTTTGTTTACT
*
870835 TTCGTTCGTTTATGTT
1 TTCGTTCGTATATGTT
870851 CGTTCATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.59
Consensus pattern (24 bp):
TTCGTTCGTATATGTTTGTTTACT
Found at i:870852 original size:14 final size:14
Alignment explanation
Indices: 870835--870864 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
870825 TTTGTTTACT
*
870835 TTCGTTCGTTTATG
1 TTCGTTCATTTATG
870849 TTCGTTCATTTATG
1 TTCGTTCATTTATG
870863 TT
1 TT
870865 TAATTCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.17, T:0.60
Consensus pattern (14 bp):
TTCGTTCATTTATG
Found at i:871070 original size:10 final size:10
Alignment explanation
Indices: 871047--871090 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
871037 GTTGTTGTGG
*
871047 TTTATATTCA
1 TTTATGTTCA
**
871057 TTTATGTTTG
1 TTTATGTTCA
*
871067 TTTACGTTCA
1 TTTATGTTCA
871077 TTTATGTTCA
1 TTTATGTTCA
871087 TTTA
1 TTTA
871091 CGTTTGTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (10 bp):
TTTATGTTCA
Found at i:871101 original size:20 final size:20
Alignment explanation
Indices: 871053--871094 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
871043 GTGGTTTATA
**
871053 TTCATTTATGTTTGTTTACG
1 TTCATTTATGTTCATTTACG
871073 TTCATTTATGTTCATTTACG
1 TTCATTTATGTTCATTTACG
871093 TT
1 TT
871095 TGTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:871256 original size:6 final size:6
Alignment explanation
Indices: 871240--871276 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
871230 GACACCAAGG
871240 CCCATCA CCCACA CCCACA CCCACA CCCACA CCCACA
1 CCCA-CA CCCACA CCCACA CCCACA CCCACA CCCACA
871277 AGTACGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (6 bp):
CCCACA
Found at i:871462 original size:17 final size:17
Alignment explanation
Indices: 871443--871528 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
871433 AGATATAGAT
*
871443 AGGAAGAGCGATAAGGT
1 AGGAAGAGCGATAAGGA
*
871460 AGGAAGAGCGATCAGGA
1 AGGAAGAGCGATAAGGA
**
871477 AGGAAGTTCGATAAGGA
1 AGGAAGAGCGATAAGGA
**
871494 AGGAAGTTCGATAAGGA
1 AGGAAGAGCGATAAGGA
*
871511 AGGAAGAGCGATATGGA
1 AGGAAGAGCGATAAGGA
871528 A
1 A
871529 AGAGATTGGA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.42, C:0.07, G:0.38, T:0.13
Consensus pattern (17 bp):
AGGAAGAGCGATAAGGA
Found at i:874958 original size:24 final size:23
Alignment explanation
Indices: 874931--874996 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
874921 TCATATAAAT
* * *
874931 TGCACCGATGTGCCTCGTAGAATA
1 TGCACCGAAGTACCACGTAGAA-A
874955 TGCACCGAAGTACCACGTAGAAA
1 TGCACCGAAGTACCACGTAGAAA
* *
874978 TGCCCCGAAGGACCACGTA
1 TGCACCGAAGTACCACGTA
874997 TATATGTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTACCACGTAGAAA
Found at i:874985 original size:23 final size:23
Alignment explanation
Indices: 874946--875019 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
874936 CGATGTGCCT
* *
874946 CGTAGAATATGCACCGAAGTACCA
1 CGTAGAA-ATGCCCCGAAGGACCA
874970 CGTAGAAATGCCCCGAAGGACCA
1 CGTAGAAATGCCCCGAAGGACCA
* * * *
874993 CGTATATATGTCCCGAAGGACCG
1 CGTAGAAATGCCCCGAAGGACCA
875016 CGTA
1 CGTA
875020 AAACCATCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 37 0.84
24 7 0.16
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCCCCGAAGGACCA
Found at i:875849 original size:21 final size:21
Alignment explanation
Indices: 875805--875900 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
875795 TTGCAGCCTT
* *
875805 GATGCATGGATGCATAG-TAG
1 GATGCATCGATGCATAGCAAG
875825 GATGCATCGATGCATAGCAAG
1 GATGCATCGATGCATAGCAAG
875846 GATGCATCGATGCATAGCAAG
1 GATGCATCGATGCATAGCAAG
* *
875867 GATGCATCGATGCACATC-AG
1 GATGCATCGATGCATAGCAAG
875887 GATGCATCGATGCA
1 GATGCATCGATGCA
875901 CTAATTGCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 32 0.45
21 39 0.55
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATAGCAAG
Found at i:875862 original size:41 final size:41
Alignment explanation
Indices: 875805--875900 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
875795 TTGCAGCCTT
* * *
875805 GATGCATGGATGCATAG-TAGGATGCATCGATGCATAGCAAG
1 GATGCATCGATGCATAGCAAGGATGCATCGATGCACAGC-AG
*
875846 GATGCATCGATGCATAGCAAGGATGCATCGATGCACATCAG
1 GATGCATCGATGCATAGCAAGGATGCATCGATGCACAGCAG
875887 GATGCATCGATGCA
1 GATGCATCGATGCA
875901 CTAATTGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 32 0.64
42 18 0.36
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (41 bp):
GATGCATCGATGCATAGCAAGGATGCATCGATGCACAGCAG
Found at i:875989 original size:21 final size:21
Alignment explanation
Indices: 875965--876041 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
875955 TTAGTGCAGA
875965 TGCATGGATGCACTGC-AGGG
1 TGCATGGATGCACTGCAAGGG
875985 ATGCATGGATGCACTGCAAGGG
1 -TGCATGGATGCACTGCAAGGG
876007 TGCATGGATGCACTGCAAGGG
1 TGCATGGATGCACTGCAAGGG
876028 TGCATGGATGCACT
1 TGCATGGATGCACT
876042 TTGACACCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 51 0.93
22 4 0.07
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAAGGG
Found at i:877476 original size:19 final size:18
Alignment explanation
Indices: 877452--877491 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
877442 TCATTTTGAT
*
877452 TTTCAAAATCAACTTTTGC
1 TTTCAAAATCAAATTTT-C
877471 TTTCAAAATCAAATTTTC
1 TTTCAAAATCAAATTTTC
877489 TTT
1 TTT
877492 AATTTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTCAAAATCAAATTTTC
Found at i:879260 original size:20 final size:22
Alignment explanation
Indices: 879235--879274 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
879225 TGTTGTATAT
879235 AGTCG-TTGGGGATG-TTTTGG
1 AGTCGTTTGGGGATGATTTTGG
879255 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
879275 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:879400 original size:20 final size:21
Alignment explanation
Indices: 879375--879449 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 21
879365 TTATAGCCTT
* *
879375 GATGCATGGATGTATAG-AAG
1 GATGCATCGATGCATAGCAAG
879395 GATGCATCGATGCATAGCAAG
1 GATGCATCGATGCATAGCAAG
* *
879416 GATGCATCGATGCACATC-AG
1 GATGCATCGATGCATAGCAAG
879436 GATGCATCGATGCA
1 GATGCATCGATGCA
879450 CTAATTGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.62
21 19 0.38
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (21 bp):
GATGCATCGATGCATAGCAAG
Found at i:879538 original size:21 final size:22
Alignment explanation
Indices: 879512--879569 Score: 102
Period size: 21 Copynumber: 2.7 Consensus size: 22
879502 CATTAGTGCA
879512 GATGCATGGATGCACTGC-AGG
1 GATGCATGGATGCACTGCAAGG
879533 GATGCATGGATGCACTGCAAGG
1 GATGCATGGATGCACTGCAAGG
879555 G-TGCATGGATGCACT
1 GATGCATGGATGCACT
879570 TTGACACCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GATGCATGGATGCACTGCAAGG
Found at i:879685 original size:30 final size:30
Alignment explanation
Indices: 879651--879710 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
879641 AACTTTGAAT
879651 AAATTCAATTCAAATCCAAAAAT-ATTTTGC
1 AAATTCAATTCAAATCC-AAAATCATTTTGC
*
879681 AAATTCAATTCAAGTCCAAAATCATTTTGC
1 AAATTCAATTCAAATCCAAAATCATTTTGC
879711 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAATCATTTTGC
Found at i:880118 original size:2 final size:2
Alignment explanation
Indices: 880111--880140 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
880101 CTTTCACGTA
880111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
880141 TCATAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:880584 original size:20 final size:20
Alignment explanation
Indices: 880561--880599 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
880551 CTATGTATCA
880561 ATACT-TTCACATCAGTATTG
1 ATACTATTCA-ATCAGTATTG
880581 ATACTAATTCAATCAGTAT
1 ATACT-ATTCAATCAGTAT
880600 ATACACCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
ATACTATTCAATCAGTATTG
Found at i:883884 original size:22 final size:22
Alignment explanation
Indices: 883852--883900 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
883842 GTGTTTTACT
883852 GCTTTCAAATAGAAAAATAATA
1 GCTTTCAAATAGAAAAATAATA
*
883874 GCTTTCGAATAGAAAAATAATA
1 GCTTTCAAATAGAAAAATAATA
883896 GCTTT
1 GCTTT
883901 TGAAAACGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (22 bp):
GCTTTCAAATAGAAAAATAATA
Found at i:886099 original size:43 final size:43
Alignment explanation
Indices: 885971--886361 Score: 299
Period size: 43 Copynumber: 9.1 Consensus size: 43
885961 AAGGTAATTA
*
885971 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACCTTTT
* * * ** *
886014 ACGACGTTTGT-TCGAAAAATATCGCTATAGATCTAACCTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACCTTTT
* * * *
886056 GCGGCGTTTGTATCCAAAAATGTCACTATATATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACCTTTT
* * * * *
886099 GCGGCATTTGTATCAAAAAACGCCGCAATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACCTTTT
** * * * *
886142 ATGACGTTTGTATCAAAAAACG-CTGGTATAGATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGTC-GCTATAGATCTGACCTTTT
* * * * *
886185 GCGGTGTTTGTATACAAAGACG-CGACTATAGATCTGACATGTT
1 GCGGCGTTTGTATCCAAAAACGTCG-CTATAGATCTGACCTTTT
* * *
886228 GCGGCGTTTGT-TCCAAAAACATCGCTATAAATATTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGAT-CTGACCTTTT
* * * * *
886271 GAGGCGTTTGT-T-CTAAAACGCCGCTATAGATATCAACCTTTT
1 GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCT-GACCTTTT
* * * * * * * *
886313 GAGACGTTTTTTTTCCAAAAACGCCGCGATAAATCTTGACCTATT
1 GCGGCG-TTTGTATCCAAAAACGTCGCTATAGATC-TGACCTTTT
886358 GCGG
1 GCGG
886362 TATTTTTTGT
Statistics
Matches: 271, Mismatches: 67, Indels: 18
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.00
42 78 0.29
43 166 0.61
44 1 0.00
45 24 0.09
46 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACCTTTT
Found at i:886312 original size:129 final size:129
Alignment explanation
Indices: 885971--886312 Score: 372
Period size: 129 Copynumber: 2.7 Consensus size: 129
885961 AAGGTAATTA
* * ***
885971 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTACGACGTTTGTTCGAAAAATAT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTACGACGTTTGTTCAAAAAACGC
* * * * *
886036 CGCTATAGATCTAACC-TTTTGCGGCGTTTGTATCCAAAAATGTCACTATATATCTGACTTTTT
66 CGCTATAGATCTAACCTTTTTGCGGCGTTTGTATACAAAAACGTCACTATAGATCTGACATGTT
* * * *
886099 GCGGCATTTGTATCAAAAAACGCCGCAATAGATATGACCTTTTATGACGTTTGTATCAAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTACGACGTTTGT-TCAAAAAACG
* * * * *
886164 CTGGTATAGATCTGA-CTTTTTGCGGTGTTTGTATACAAAGACG-CGACTATAGATCTGACATGT
65 CCGCTATAGATCTAACCTTTTTGCGGCGTTTGTATACAAAAACGTC-ACTATAGATCTGACATGT
886227 T
129 T
** * * *
886228 GCGGCGTTTGT-TCCAAAAACATCGCTATAAATATTGACCTTTTGA-GGCGTTTGTTC-TAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATA-TGACCTTTT-ACGACGTTTGTTCAAAAAAC
*
886290 GCCGCTATAGATATCAACCTTTT
64 GCCGCTATAGATCT-AACCTTTT
886313 GAGACGTTTT
Statistics
Matches: 176, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
127 16 0.09
128 71 0.40
129 88 0.50
130 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (129 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTACGACGTTTGTTCAAAAAACGC
CGCTATAGATCTAACCTTTTTGCGGCGTTTGTATACAAAAACGTCACTATAGATCTGACATGTT
Found at i:890101 original size:21 final size:21
Alignment explanation
Indices: 890076--890120 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
890066 CACAAAGAAG
890076 TATGATCCTTACTTAAATACC
1 TATGATCCTTACTTAAATACC
890097 TATGATCCTTACTTAAATACC
1 TATGATCCTTACTTAAATACC
890118 TAT
1 TAT
890121 AATACAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (21 bp):
TATGATCCTTACTTAAATACC
Found at i:891894 original size:11 final size:11
Alignment explanation
Indices: 891880--891905 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
891870 TTTTCGTTCT
891880 TTTTATTTTTA
1 TTTTATTTTTA
891891 TTTTATTTTTA
1 TTTTATTTTTA
891902 TTTT
1 TTTT
891906 TTCCTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:893125 original size:15 final size:15
Alignment explanation
Indices: 893107--893145 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
893097 AAAGAAAGAG
893107 AAAAAAAATCGTGCA
1 AAAAAAAATCGTGCA
* *
893122 AAAAAAGATTGTGCA
1 AAAAAAAATCGTGCA
893137 AAAAGAAAA
1 AAAA-AAAA
893146 GAAAAAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.64, C:0.08, G:0.15, T:0.13
Consensus pattern (15 bp):
AAAAAAAATCGTGCA
Found at i:898123 original size:30 final size:30
Alignment explanation
Indices: 898087--898161 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
898077 GCCTTCCAGC
*
898087 GGACTTAATGCTAGCGGCCTTACGGCCAAA
1 GGACTTAATGCTAGAGGCCTTACGGCCAAA
* *
898117 GGACTTAATGCTAGAGGCCTTACTGCCAGA
1 GGACTTAATGCTAGAGGCCTTACGGCCAAA
* *
898147 CGACTTGATGCTAGA
1 GGACTTAATGCTAGA
898162 AGCCATACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (30 bp):
GGACTTAATGCTAGAGGCCTTACGGCCAAA
Found at i:898138 original size:15 final size:15
Alignment explanation
Indices: 898087--898161 Score: 51
Period size: 15 Copynumber: 5.0 Consensus size: 15
898077 GCCTTCCAGC
*
898087 GGACTTAATGCTAGC
1 GGACTTAATGCTAGA
* ** * *
898102 GGCCTTACGGCCAAA
1 GGACTTAATGCTAGA
898117 GGACTTAATGCTAGA
1 GGACTTAATGCTAGA
* * *
898132 GGCCTTACTGCCAGA
1 GGACTTAATGCTAGA
* *
898147 CGACTTGATGCTAGA
1 GGACTTAATGCTAGA
898162 AGCCATACTG
Statistics
Matches: 41, Mismatches: 19, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (15 bp):
GGACTTAATGCTAGA
Found at i:898171 original size:30 final size:30
Alignment explanation
Indices: 898088--898183 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
898078 CCTTCCAGCG
** * * * *
898088 GACTTAATGCTAGCGGCCTTACGGCCAAAG
1 GACTTAATGCTAGAAGCCATACTGCCAGAC
* *
898118 GACTTAATGCTAGAGGCCTTACTGCCAGAC
1 GACTTAATGCTAGAAGCCATACTGCCAGAC
* * *
898148 GACTTGATGCTAGAAGCCATACTGCCGGAG
1 GACTTAATGCTAGAAGCCATACTGCCAGAC
898178 GACTTA
1 GACTTA
898184 GACAACTGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (30 bp):
GACTTAATGCTAGAAGCCATACTGCCAGAC
Found at i:921495 original size:45 final size:45
Alignment explanation
Indices: 921436--921809 Score: 473
Period size: 45 Copynumber: 8.3 Consensus size: 45
921426 CAAATTGGCG
* *
921436 TAAAAGATGTCACTAATGAAAATGCATAACGGTGCATTATCGACA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
* * *
921481 TAAAAGGTGCCACTAATGAAAATGCATAACGGTTCATTATCAAAA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
* **
921526 TAAAAGGTGCCACTAATGAAAATTCATAACGGTGCATTATCGGTA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
* * *
921571 TAAAATGTGCCATTAATGAAAGTGCATAACGGTGCATTATCGGA-A
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC-GACA
* * * *
921616 TAAATGGTTCCACTAATGAAAATGCATAACAGTGCATTATCGGCA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
*
921661 TAAAATGTGCCACTAATGAAAATGCATAACGGTGCATTATC-ATCA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGA-CA
* * *
921706 TAAAAGGCGACACTAATGAAAATGCATAACGGTGCATTATCAACA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
* * ** * **
921751 TAAAAGGTGCCACTAATAAAAATACATTTCGGTGCATTATAGGTA
1 TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
*
921796 TAGAAGGTGCCACT
1 TAAAAGGTGCCACT
921810 CATGGTATTC
Statistics
Matches: 284, Mismatches: 41, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
44 1 0.00
45 281 0.99
46 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (45 bp):
TAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGACA
Found at i:921560 original size:25 final size:25
Alignment explanation
Indices: 921486--921560 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
921476 CGACATAAAA
*
921486 GGTGCCACTAATGAAAATGCATAAC
1 GGTGCCACTAATGAAAATTCATAAC
* * * *
921511 GGT-TCA-TTATCAAAA-T-A-AAA
1 GGTGCCACTAATGAAAATTCATAAC
921531 GGTGCCACTAATGAAAATTCATAAC
1 GGTGCCACTAATGAAAATTCATAAC
921556 GGTGC
1 GGTGC
921561 ATTATCGGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 5 0.14
21 3 0.08
22 7 0.19
23 8 0.22
24 3 0.08
25 10 0.28
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (25 bp):
GGTGCCACTAATGAAAATTCATAAC
Found at i:922061 original size:2 final size:2
Alignment explanation
Indices: 922054--922079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
922044 AGTAGCCATG
922054 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
922080 GCATGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:924928 original size:15 final size:15
Alignment explanation
Indices: 924907--924943 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
924897 AATAGACAGT
924907 AAAAGTGAAAAGAGA
1 AAAAGTGAAAAGAGA
* *
924922 GAAAGTGAAAAGTGA
1 AAAAGTGAAAAGAGA
924937 AAAAGTG
1 AAAAGTG
924944 GGGTAGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (15 bp):
AAAAGTGAAAAGAGA
Found at i:933362 original size:11 final size:12
Alignment explanation
Indices: 933331--933362 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
933321 ATTACGTTAG
933331 AAGAAGAAAATA
1 AAGAAGAAAATA
933343 AAGAAGAAAATA
1 AAGAAGAAAATA
933355 AA-AAGAAA
1 AAGAAGAAA
933363 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAGAAGAAAATA
Found at i:934958 original size:116 final size:115
Alignment explanation
Indices: 934672--935019 Score: 346
Period size: 116 Copynumber: 3.0 Consensus size: 115
934662 GTAGACAAAA
* * * * *
934672 ATTTCCACTGGAAGGGTTCATAATAAG--AACTCATCCAATGAGGGACAAAAACTTCCTAATGAG
1 ATTTCCAGTAGAAGGGTTCATAATAAGAAAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAG
** * * * * *
934735 AAGAACTTGTTCATTCTAGACTCGT-CCATCACAGAAGAAGGACGAGTCAAC
66 AAGAACTTGTTCAACCTTGACTC-TACCATCACATAAGGA-GATGAATCAAC
* * * *
934786 ATTTCCAGTAGAAGGGTTCATAATGAGAAGAACTCATCCAATGATGAAGAAGAAGTTCATAATGA
1 ATTTCCAGTAGAAGGGTTCATAATAAGAA-AACTCATCCAATGAGGGAGAAGAAGTTCCTAATGA
* *
934851 CAAGAACTTGTTCAACCTTGACTCTACCATCACATAAGGAGATGAATCAAT
65 GAAGAACTTGTTCAACCTTGACTCTACCATCACATAAGGAGATGAATCAAC
* ** * *
934902 GTTTTTA-TTGAAAGGGTTCATAATAAGAAAAACTTATCCAATGAGGGAGAAGAAGTTCCTAATG
1 ATTTCCAGTAG-AAGGGTTCATAATAAG-AAAACTCATCCAATGAGGGAGAAGAAGTTCCTAATG
* * * ** *
934966 AGAATAACTTATTCAACCTTGGCTC-ATCCATCATGTAAGGAGATGAACCAAC
64 AGAAGAACTTGTTCAACCTTGACTCTA-CCATCACATAAGGAGATGAATCAAC
935018 AT
1 AT
935020 CATCTTTGTG
Statistics
Matches: 191, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
114 24 0.13
115 3 0.02
116 101 0.53
117 63 0.33
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (115 bp):
ATTTCCAGTAGAAGGGTTCATAATAAGAAAACTCATCCAATGAGGGAGAAGAAGTTCCTAATGAG
AAGAACTTGTTCAACCTTGACTCTACCATCACATAAGGAGATGAATCAAC
Found at i:936341 original size:19 final size:20
Alignment explanation
Indices: 936317--936354 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
936307 CAGGTTAATG
*
936317 GTCAACGGTC-AAAGTCAAA
1 GTCAACGATCAAAAGTCAAA
936336 GTCAACGATCAAAAGTCAA
1 GTCAACGATCAAAAGTCAA
936355 TGATCGGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (20 bp):
GTCAACGATCAAAAGTCAAA
Found at i:936395 original size:26 final size:26
Alignment explanation
Indices: 936361--936411 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
936351 TCAATGATCG
*
936361 GAGTTAACGAATCGATCAAACGGGTC
1 GAGTCAACGAATCGATCAAACGGGTC
* *
936387 GAGTCAACGGATCGATCAAATGGGT
1 GAGTCAACGAATCGATCAAACGGGT
936412 TCATGGGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (26 bp):
GAGTCAACGAATCGATCAAACGGGTC
Found at i:939336 original size:20 final size:19
Alignment explanation
Indices: 939294--939337 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
939284 AAGCATGTAC
*
939294 TTTCATTAAAATCATATAT
1 TTTCATTAAAATCATATAA
939313 TTTCATTAAAAATCA-AGTAA
1 TTTCATT-AAAATCATA-TAA
939333 TTTCA
1 TTTCA
939338 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTCATTAAAATCATATAA
Found at i:940339 original size:59 final size:59
Alignment explanation
Indices: 940172--940345 Score: 169
Period size: 59 Copynumber: 3.0 Consensus size: 59
940162 TGTTTACCAA
* * * *
940172 ATGGAGCAATTTGTGTGCTAAAATGATAAGGAAA-CTATACTGAGTGTATAGATTTCCAT
1 ATGGAGCACTTAGTGTGCTAAAATGATAAGGAAATC-ATACAGAGTGTATGGATTTCCAT
* * ***
940231 ATGGAGCACTTAGTGTACT-AAATGATAAGGAAATCATATTA-AAAATATGGATTTCCAT
1 ATGGAGCACTTAGTGTGCTAAAATGATAAGGAAATCATA-CAGAGTGTATGGATTTCCAT
* * *
940289 ATAGG-GCATGTTA-TGTGCTAAAATGGTAAGGAAATCATACAGGGTGTATGGATTTCC
1 AT-GGAGCA-CTTAGTGTGCTAAAATGATAAGGAAATCATACAGAGTGTATGGATTTCC
940346 CAGGTAAAGC
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
58 41 0.45
59 51 0.55
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (59 bp):
ATGGAGCACTTAGTGTGCTAAAATGATAAGGAAATCATACAGAGTGTATGGATTTCCAT
Found at i:940489 original size:59 final size:59
Alignment explanation
Indices: 940379--940490 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
940369 CAAGGATAAG
* * *
940379 AAAATCAAACTAATGGTATGGATTTTCACATAGGGCATTTTATGTGATAAAATGGTAAC
1 AAAATCAAACTAATGGTATGAATTTTCACATAGGGCACTTCATGTGATAAAATGGTAAC
* * * *
940438 AAAATCATACTAATGGTATGAATTTTTGA-ATAGGGCACTTCGTGTGCTAAAAT
1 AAAATCAAACTAATGGTATGAA-TTTTCACATAGGGCACTTCATGTGATAAAAT
940491 AAAAGAGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 40 0.89
60 5 0.11
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (59 bp):
AAAATCAAACTAATGGTATGAATTTTCACATAGGGCACTTCATGTGATAAAATGGTAAC
Found at i:941100 original size:22 final size:23
Alignment explanation
Indices: 941072--941114 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
941062 TGCACTGTTC
*
941072 ACTGTTCAC-GGTACTGTTCACT
1 ACTGTTCACGGGTACTATTCACT
941094 ACTGTTCACGGGTACTATTCA
1 ACTGTTCACGGGTACTATTCA
941115 TAAAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (23 bp):
ACTGTTCACGGGTACTATTCACT
Found at i:945665 original size:11 final size:11
Alignment explanation
Indices: 945626--945678 Score: 70
Period size: 11 Copynumber: 4.8 Consensus size: 11
945616 TTGCTGGAAA
945626 TACTGTAGCAG
1 TACTGTAGCAG
* * *
945637 TATTGTAGTAT
1 TACTGTAGCAG
*
945648 TATTGTAGCAG
1 TACTGTAGCAG
945659 TACTGTAGCAG
1 TACTGTAGCAG
945670 TACTGTAGC
1 TACTGTAGC
945679 TATGCATCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (11 bp):
TACTGTAGCAG
Found at i:951929 original size:2 final size:2
Alignment explanation
Indices: 951922--951956 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
951912 GGCTCATGAC
951922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
951957 TAAGTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:956250 original size:18 final size:17
Alignment explanation
Indices: 956226--956272 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
956216 GGCAGTTGAC
956226 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* * *
956243 TCATTTAAATTGGTTCAT
1 T-AATTAAACTAGTTCAT
956261 TAATTAAACTAG
1 TAATTAAACTAG
956273 CTCTTTATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:959362 original size:17 final size:17
Alignment explanation
Indices: 959311--959364 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
959301 GGTAGTTGAC
959311 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* * *
959328 TCATTTAAAATGGTTCAT
1 T-AATTAAACTAGTTCAT
*
959346 TAATTAAACTAGATCAT
1 TAATTAAACTAGTTCAT
959363 TA
1 TA
959365 TATTTTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:959395 original size:5 final size:5
Alignment explanation
Indices: 959385--959411 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
959375 CATAACATGT
959385 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
959412 CAAGCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:960555 original size:11 final size:12
Alignment explanation
Indices: 960528--960557 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
960518 CGGTTTAGCA
960528 AAAAAACAAAAG
1 AAAAAACAAAAG
960540 AAAAAACAAAAG
1 AAAAAACAAAAG
960552 AAAAAA
1 AAAAAA
960558 AAGTTTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAG
Found at i:961900 original size:18 final size:17
Alignment explanation
Indices: 961876--961922 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
961866 GGTAGTTGAC
961876 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* * *
961893 TCATTTAAAGTGGTTCAT
1 T-AATTAAACTAGTTCAT
961911 TAATTAAACTAG
1 TAATTAAACTAG
961923 CTCTTTATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:961959 original size:5 final size:5
Alignment explanation
Indices: 961949--961980 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
961939 CATAACATGT
961949 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
961981 CAAGCTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:963271 original size:12 final size:12
Alignment explanation
Indices: 963254--963283 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
963244 CGGTTTAGCA
963254 AAAAAACAAAAG
1 AAAAAACAAAAG
963266 AAAAAACAAAAG
1 AAAAAACAAAAG
963278 AAAAAA
1 AAAAAA
963284 AAAGTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAG
Found at i:964627 original size:18 final size:17
Alignment explanation
Indices: 964603--964649 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
964593 GGTAGTTGAC
964603 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* * *
964620 TCATTTAAAATGGTTCAT
1 T-AATTAAACTAGTTCAT
964638 TAATTAAACTAG
1 TAATTAAACTAG
964650 CTCTTTATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:967347 original size:18 final size:17
Alignment explanation
Indices: 967323--967369 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
967313 GGTAGTTGAC
967323 TAATTAAACTAGTTCAT
1 TAATTAAACTAGTTCAT
* * *
967340 TCATTTAAAATGGTTCAT
1 T-AATTAAACTAGTTCAT
967358 TAATTAAACTAG
1 TAATTAAACTAG
967370 CTCTTTATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
TAATTAAACTAGTTCAT
Found at i:967406 original size:5 final size:5
Alignment explanation
Indices: 967396--967427 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
967386 CAAAACATGT
967396 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
967428 CAAGATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:968509 original size:20 final size:20
Alignment explanation
Indices: 968484--968534 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
968474 TGCAGTGGCA
968484 AAATGGAATGGATGTGGTGG
1 AAATGGAATGGATGTGGTGG
968504 AAATGGAATGGATGTGGTGG
1 AAATGGAATGGATGTGGTGG
968524 AAATGGAATGG
1 AAATGGAATGG
968535 TGATAGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (20 bp):
AAATGGAATGGATGTGGTGG
Found at i:972460 original size:110 final size:110
Alignment explanation
Indices: 972242--972480 Score: 238
Period size: 110 Copynumber: 2.2 Consensus size: 110
972232 TGATTTGGTG
* * * *
972242 CTTAATCATATGTCATTGAT-CTAGTTAATCTAGTTTTCTTGCTGAAATTTATTTCTTTCTTCAC
1 CTTAATCATAAGTCAATG-TGC-AGTTAATCTAGTTTCCTTGCTGAAATTTATTTCTTTATTCAC
* ** *
972306 TTGTTAGGTACACTACAATGTTAAATTAGTGTTTTGATAGTTTGATA
64 TAGTTAGGTACACTACAATACTAAATTAGTGTTTGGATAGTTTGATA
*
972353 CTTAATCAT-AGTTCAATGTGCAGTTAATCTAGTTTCCTTGTTGAAATTTATTTCTTTATT-AC-
1 CTTAATCATAAG-TCAATGTGCAGTTAATCTAGTTTCCTTGCTGAAATTTATTTCTTTATTCACT
* * * * *
972415 AGTTACATGTACATTACAATACTCAATTCGT-TTTGGGAT-GATTTGATG
65 AGTT--AGGTACACTACAATACTAAATTAGTGTTT-GGATAG-TTTGATA
*
972463 CTTCATCATAAGTCAATG
1 CTTAATCATAAGTCAATG
972481 CGTGGTACAG
Statistics
Matches: 106, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
108 3 0.03
109 6 0.06
110 80 0.75
111 17 0.16
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (110 bp):
CTTAATCATAAGTCAATGTGCAGTTAATCTAGTTTCCTTGCTGAAATTTATTTCTTTATTCACTA
GTTAGGTACACTACAATACTAAATTAGTGTTTGGATAGTTTGATA
Found at i:975070 original size:13 final size:13
Alignment explanation
Indices: 975049--975100 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
975039 AATGACGCGC
*
975049 AATGAGCGTCATA
1 AATGCGCGTCATA
975062 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
975075 AATGTGTGTCATA
1 AATGCGCGTCATA
*
975088 AATGCGAGTCATA
1 AATGCGCGTCATA
975101 GATTTATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:975078 original size:26 final size:26
Alignment explanation
Indices: 975049--975100 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
975039 AATGACGCGC
*
975049 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGAGTCATA
* *
975075 AATGTGTGTCATAAATGCGAGTCATA
1 AATGAGCGTCATAAATGCGAGTCATA
975101 GATTTATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGAGTCATA
Found at i:976599 original size:18 final size:18
Alignment explanation
Indices: 976575--976621 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
976565 GGTAGTTGAC
976575 TAATTAAACTAG-TTCAT
1 TAATTAAACTAGATTCAT
* *
976592 TCATTTAAAAT-GATTCAT
1 T-AATTAAACTAGATTCAT
976610 TAATTAAACTAG
1 TAATTAAACTAG
976622 CTCTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (18 bp):
TAATTAAACTAGATTCAT
Found at i:978292 original size:15 final size:16
Alignment explanation
Indices: 978272--978302 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
978262 GGAGTGTTTG
978272 GTGAGGTT-TTTTTTT
1 GTGAGGTTATTTTTTT
978287 GTGAGGTTATTTTTTT
1 GTGAGGTTATTTTTTT
978303 TACTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.10, C:0.00, G:0.26, T:0.65
Consensus pattern (16 bp):
GTGAGGTTATTTTTTT
Done.